Saint Thomas's fine natural harbor became known as "Taphus" for the drinking establishments located nearby. ("Tap Hus" translates as "rum shop" or "tap house" referring to the drinking establishments.[2]) In 1691, the primary settlement there was renamed Charlotte Amalie in honor of the wife of Denmark's King Christian V. It was later declared a free port by Frederick V. In December 1732, the first two of many Moravian Brethren missionaries came from HerrnhutSaxony in present-day Germany to minister to them. Distrusted at first by the white masters, they lived among the slaves and soon won their confidence.[3]

The first British invasion and occupation of the Danish West Indies occurred at the end of March 1801 when a British fleet arrived at St Thomas. The Danes accepted the Articles of Capitulation the British proposed and the British occupied the islands without a shot being fired. The British occupation lasted until April 1802, when the British returned the islands to Denmark.

The second British invasion of the Danish West Indies took place in December 1807 when a British fleet captured St Thomas on 22 December and Santa Cruz on 25 December. The Danes did not resist and the invasion was bloodless. This British occupation of the Danish West Indies lasted until 20 November 1815, when Britain returned the islands to Denmark.

While the sugar trade had brought prosperity to the island's free citizens, by the early 19th century Saint Thomas was in decline. The continued export of sugar was threatened by hurricanes, drought, and American competition. Following the Danish Revolution of 1848, slavery was abolished and the resulting rise in labor costs further weakened the position of Saint Thomas's sugar producers.

Given its harbors and fortifications, Saint Thomas still retained a strategic importance, and thus, in the 1860s, during the American Civil War and its aftermath, the United States government considered buying the island and its neighbors from Denmark for $7.5 million. However, the proponents of the purchase failed to gain legislative support for the bid.

As the islands were poorly managed by the Danes, a local islander, David Hamilton Jackson, was instrumental in persuading the Danish to allow the US to purchase the islands of St. Thomas, St. John, and St. Croix. In 1915, he traveled to Denmark and convinced the King of Denmark to allow freedom of the press in the islands.[5] He began the first newspaper in the islands, known as The Herald. After this, he organized labor unions among the islanders for better working conditions. The islands now have an annual celebration to honor the legacy of David Hamilton Jackson.[6]

In 1917, St. Thomas was purchased (along with Saint John and Saint Croix) by the United States for $25 million in gold,[7] as part of a defensive strategy to maintain control over the Caribbean and the Panama Canal during the First World War. The transfer occurred on March 31, 1917, behind Fort Christian before the barracks that now house the Legislature of the U.S Virgin Islands. The baccalaureate service for the transfer was held at the St. Thomas Reformed Church as it was identified as the American church in the Danish West Indies.

Percival Wilson Sparks, a U.S. Naval officer, designed the flag that now represents the United States Virgin Islands. Sparks married a local U.S Virgin Island woman, Grace Joseph Sparks; when Sparks' superior, Rear Adm. Summer Ely Wetmore Kitelle, commissioned the design for the flag, P. W. Sparks asked his wife and her sister, Blanche Joseph (later Sasso), to sew the first flag. That flag was used until such time as a factory-produced flag could be acquired.

The flag's inspiration came from the U.S. Presidential seal. Sparks decided to have the eagle facing the olive branches (which represented peace) rather than the arrows (which represented the three islands: St. Croix, St. Thomas, and St. John). (At the request of Emilie Rose Sparks Gray, a daughter of P.W. Sparks and Grace Sparks, so that the family would have clear and undeniable proof, this piece of history was entered into the Congressional Record in Washington, D.C., on April 30, 1986,[8] by the congressional delegate, Ron de Lugo.) Every year Transfer Day is recognized as a holiday, to celebrate the acquisition of the islands by the United States in 1917.

U.S. citizenship was granted to the residents in 1927. The U.S. Department of the Interior took over administrative duties in 1931. American forces were based on the island during the Second World War. In 1954, passage of the U.S. Virgin Islands Organic Act officially granted territorial status to the three islands, and allowed for the formation of a local senate with politics dominated by the American Republican and Democratic parties. Full home rule was achieved in 1970.

The post-war era also saw the rise of tourism on the island. With relatively cheap air travel and the American embargo on Cuba, the numbers of visitors greatly increased. Despite natural disasters such as Hurricane Hugo (1989) and Hurricanes Luis and Marilyn (1995), the island's infrastructure continues to improve as the flow of visitors continues. Hotels have been built from the West End to the East End.

Passenger and limited car-ferry services to neighboring islands such as Water Island, St. John, St. Croix, and the British Virgin Islands run regularly out of the Red Hook Terminal, Charlotte Amalie, and Crown Bay Marina.

The United States Virgin Islands is the only place under United States jurisdiction where the rule of the road is to drive on the left. This was inherited from what was the then-current Danish practice at the time of the American acquisition in 1917. However, because St. Thomas is a U.S. territory, most cars are imported from the mainland United States and therefore the steering column is located on the left side of the vehicle.

The island has many regular taxis from compact size to large vans, as well as open-air, covered trucks called "safaris" with bench seats. The latter usually operate only between high-traffic points, e.g., cruise-ship terminals at Havensight and Crown Bay and downtown Charlotte Amalie.